Table 2.

Top 10 variants ranked by ascending experiment-wise P value based on analysis of the association of allele frequency with heroin addiction in the Caucasian group

Rank Order		Allele frequency, Aa		Experiment- wise Pb		Variant locationc	Distance (bases)
	Variant	Control	Case		Cytoband			Gene	Gene description
1	rs10494334	0.18	0.23	0.035	1q23.3
2	rs2323218	0.18	0.25	0.221	6q27	downd	8,989	T	T, brachyury homolog
3	rs7923687	0.83	0.79	0.426	10q25.1
4	rs6121489	0.03	0.05	0.523	20q13.33	introne		CDH4	cadherin 4, type 1, R-cadherin (retinal)
5	rs3849399	0.78	0.71	0.605	2p24.1
6	rs9271	0.75	0.68	0.620	17q25.3	3′UTRf		WDR45L	DR45-like
7	rs10518620	0.89	0.84	0.632	4q28.3
8	rs3893249	0.79	0.72	0.640	2p24.1
9	rs1711055	0.30	0.25	0.736	15q22.1	intron		AQP9	aquaporin 9
10	rs724729	0.73	0.63	0.741	15q14

^aA allele is defined by Affymetrix and can be found at the NetAffx Analysis Center (http://www.affymetrix.com/analysis/index.affx).

^bPoint-wise P value was 0.0003 for all the alleles listed. The t statistic of the observed data was calculated and then the case/control labels of each subject were permuted. For each permutation, a t statistic was obtained. For a sample size of 14 with 8 cases and 6 controls, there are 3,003 total possible permutations. The value 0.0003 was obtained when the observed t statistic is the smallest among 3,003 t statistics (1/3,003 = 0.0003). The originally observed t statistic was compared to the distribution of t statistics composed of 3,003 maximum t statistics to obtain the experiment-wise P value.

^cVariant location is given when variant is found with 100,000 nucleotides of an annotated gene.

^ddown = distance the variant is located downstream of the polyadenylation site of the specified gene.

^eintron = variant is located in the intron of specified gene.

^f3′UTR = variant is located in the 3; untranslated region of the specified gene.

Data is from the NetAffx web site; verified and corrected using the USCS Genome Browser.